(if low_prev = TRUE, this step is skipped)
### If only high-prevalence clones being displayed, remove microbiopsies without any clones >0.01 (otherwise mapscape fails)
if (low_prev == FALSE) {
print("removing low prevelence (<0.01) samples from display")
max_prev <- prev_tbl_filt %>%
dplyr::group_by(sample_id) %>%
dplyr::summarise(max_prev = max(clonal_prev))
high_prev_samples <- max_prev %>%
dplyr::filter(max_prev >= 0.03) %>%
dplyr::select(sample_id)
removed_samps <- max_prev %>%
dplyr::filter(max_prev < 0.03) %>%
dplyr::select(sample_id)
removed_samps <- removed_samps$sample_id
high_prev_samples <- high_prev_samples$sample_id
print(removed_samps)
prev_tbl_filt <- prev_tbl_filt %>%
dplyr::filter(sample_id %in% high_prev_samples)
location_tbl <- location_tbl %>%
dplyr::filter(sample_id %in% high_prev_samples)
# filter mut table to only inclde samples/clones present
present_clones <- unique(prev_tbl_filt$clone_id)
if (exists("mut_tbl_final")) {
mut_tbl_final <- mut_tbl_final %>%
dplyr::filter(sample_id %in% high_prev_samples,
clone_id %in% present_clones)
}
} else {
print("Low prevelence clones displayed, entire tree included")
}
## [1] "removing low prevelence (<0.01) samples from display"
## factor()
## 15 Levels: b_0049 b_0052 b_0054 b_0056 b_0059 b_0065 b_0072 b_0075 ... b_0095
cluster_diagram_file <- paste0(ndp_dir, "/Cluster_and_spectrum_plots.pdf")
mut_counts %>%
kable %>%
kable_styling("striped", full_width = F) %>%
scroll_box(width = "300px", height = "500px")
| Cluster ID | Mutations Assigned |
|---|---|
| Cl.1 | 1125 |
| Cl.2 | 2677 |
| Cl.3 | 1764 |
| Cl.4 | 345 |
| Cl.5 | 2670 |
| Cl.6 | 284 |
| Cl.7 | 344 |
| Cl.8 | 1212 |
| Cl.9 | 427 |
| Cl.10 | 3505 |
| Cl.13 | 3455 |
| Cl.14 | 3891 |
| Cl.15 | 2736 |
| Cl.16 | 1071 |
| Cl.17 | 4733 |
| Cl.18 | 1232 |
| Cl.21 | 2234 |
| Cl.24 | 173 |
| Cl.26 | 3041 |
| Cl.27 | 217 |
| Cl.31 | 3172 |
| Cl.32 | 605 |
| Cl.33 | 1201 |
| Cl.34 | 359 |
| Cl.36 | 3325 |
| Cl.37 | 1277 |
if (exists("mut.file")) {
print("mutation table found")
mapscape(clonal_prev = prev_tbl_filt,
tree_edges = edge_tbl,
sample_locations = location_tbl,
img_ref = image.file,
static_tree_image = static_tree_file,
width = 1500,
height = 1300,
show_low_prev_gtypes = low_prev,
phylogeny_title = sample_name,
anatomy_title = pat_age,
clone_colours = color_tbl,
mutations = mut_tbl_final)
} else {
print("no mutation table found")
mapscape(clonal_prev = prev_tbl_filt,
tree_edges = edge_tbl,
sample_locations = location_tbl,
img_ref = image.file,
static_tree_image = static_tree_file,
width = 1500,
height = 1300,
show_low_prev_gtypes = low_prev,
phylogeny_title = sample_name,
clone_colours = color_tbl)
}
## [1] "mutation table found"
## [1] "[WARNING] Low prevalence genotypes will not be shown in the view. To show them, set show_low_prev_gtypes parameter to TRUE."